I figured that it would be an all-or-nothing swap, using the brakes, hubs, etc from the Titan. Hadn't gotten to the point of counting splines on the ends of the axles yet, so haven't looked to see if the spline count is the same or not, and if it isn't then it would require more consideration.I came from a Hardbody as well, as the new bolt pattern really pissed me off when I first bought my truck. However I am over it now and it doesn't bother me anymore. I could see if you were shopping for used or new aftermarket wheels that can be an issue and limit your selection. Or if you had a bunch of wheel from your HB that you wanted to use on the D40. However the 6x4.5" pattern is not that rare. Dodges use it for their mid size trucks and SUVs. Dakotas and Durangns.
As for the knuckles. Yes they are swappable. I think the main issue is the hub and CV axle interface. I think the splines and ends are different. You would have to also swap in a m205 diff. Brakes are different too (?).
As for the rear axle, in the street car world it's not uncommon to have a truck Dana60 cut-down to fit into muscle cars, and works well so long as the existing axle shafts don't taper-down past the splines, so the splines can be machined further down the axle before the axle is shortened to match the cut-down housing. Unfortunately if an axle shaft does have that taper then it requires new ones from scratch. I have not yet compared the rears to see if the Titan's caliper mounts are the same as a Frontier's or not, if they are then it would be taking Titan axle shafts, having them cut down and splined to fit the Frontier axle, then using the Titan brakes if they bolt-up. If they don't use the same caliper mounts then it's having a Titan axle narrowed, with the shock mounts and perches moved out to the right distance for the leafsprings. The rear end is considerably easier than the front though, as performance shops are already used to doing this rear axle work.